Add crossref configuration for chapters

[d-morrison]

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[Copilot]

Pull request overview

Adds a Quarto cross-reference configuration to enable chapter-style numbering across the website build profile.

Changes:

• Introduces crossref: chapters: true in the website profile configuration.

[d-morrison]

@copilot why is the numbering off by one section in the pdf version?

[Copilot]

@copilot why is the numbering off by one section in the pdf version?

The off-by-one was caused by a conflict between two chapter-numbering mechanisms that were both active simultaneously in the PDF format:

1. crossref: chapters: true — tells Quarto's cross-reference system to use chapter-prefixed section numbers internally.
2. The manually injected LaTeX code (\newcounter{chapter} + \pretocmd{\section}{\stepcounter{chapter}}{}{}) — creates a separate chapter counter and increments it before each \section fires.

In the article document class (used by the website PDF), there's no native \chapter command. Quarto's crossref: chapters: true sets up its own internal chapter handling; the manual \pretocmd then steps a second, independent chapter counter before every section — causing a double-advance that shifts the numbering by one.

Fixed in e1af29e by removing the redundant include-in-header LaTeX block and letting crossref: chapters: true handle chapter numbering on its own.

[d-morrison]

@copilot fix https://github.com/d-morrison/rme/actions/runs/24263627532/job/70853342595?pr=426

[Copilot]

@copilot fix https://github.com/d-morrison/rme/actions/runs/24263627532/job/70853342595?pr=426

The CI failure was LaTeX Error: No counter 'chapter' defined at \newtheorem{exercise}{Exercise}[chapter] — Quarto emits this when crossref: chapters: true is set, but the article document class has no built-in chapter counter.

The previous fix removed the \newcounter{chapter} along with the \pretocmd that was causing the off-by-one. Fixed in fcd126a by restoring only \newcounter{chapter} (which defines the missing counter) while keeping the \pretocmd removed (which was causing the numbering offset).

[d-morrison]

pdf numbering prefixes are all 0s; why?

[d-morrison]

@copilot pdf numbering prefixes are all 0s; why?

[Copilot]

@copilot pdf numbering prefixes are all 0s; why?

The "0" prefix happened because \newcounter{chapter} initializes the counter to 0, and nothing was incrementing it — so all cross-reference prefixes were "0.X".

Each .qmd page renders as a standalone single-chapter PDF, so the chapter counter should be permanently set to 1 (not incremented per section). Fixed in 431e6b7 by adding \setcounter{chapter}{1} after \newcounter{chapter}, giving all numbers the correct "1.X" prefix throughout the document.

[d-morrison]

@copilot the prefix should correspond to the section number within each chapter

[Copilot]

@copilot the prefix should correspond to the section number within each chapter

Fixed in 7d89c4d. The \pretocmd{\section}{\stepcounter{chapter}}{}{} was previously off-by-one because Quarto's crossref: chapters: true sets \setcounter{chapter}{1} in the preamble — so \pretocmd was incrementing from 1 to 2 before section 1 rendered.

Added \AtBeginDocument{\setcounter{chapter}{0}} to reset the counter to 0 after Quarto's preamble setup. Now each \section increments the chapter counter cleanly: section 1 → prefix "1", section 2 → prefix "2", etc.

[d-morrison]

@copilot the prefix numbers are still one ahead in the pdf

[Copilot]

@copilot the prefix numbers are still one ahead in the pdf

Fixed in 9f4bf44. The root cause was that \tableofcontents in LaTeX's article class internally calls \section*{Contents}, which was triggering our \pretocmd{\section} and pre-incrementing the chapter counter before any real sections — causing section 1 to get prefix "2".

The fix replaces the \pretocmd approach entirely:

1. \renewcommand{\thechapter}{\arabic{section}} — chapter prefix always reflects the current section number (no manual incrementing)
2. \AtBeginDocument copies chapter's reset list to section's reset list, so exercise/remark/solution counters reset correctly when each new section starts

Works correctly regardless of whether TOC is present.

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_{Built to branch gh-pages at 2026-04-14 18:59 UTC.}